Contacts of the helix formed by residues 354 - 372 (chain A) in PDB entry 4I2F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 354 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A GLU 4.8 3.6 - - - +
353A ALA* 1.3 77.0 - - - +
355A GLU* 1.4 60.1 + - - +
356A ASP* 3.7 6.8 + - - +
357A GLU* 3.1 36.7 + - - +
358A GLU* 3.0 28.9 + - - +
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Residues in contact with GLU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A THR* 1.4 73.9 - - - +
356A ASP* 1.3 61.9 + - - +
358A GLU* 3.5 14.1 - - - +
359A GLN* 3.2 25.6 + - - +
387A LYS* 5.4 8.7 - - - +
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Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A THR* 3.3 6.5 + - - +
355A GLU* 1.3 80.0 - - - +
357A GLU* 1.4 59.6 + - - +
359A GLN* 3.1 9.8 + - - +
360A GLN* 3.0 34.5 + - + +
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Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE 5.2 2.3 - - - +
323A LEU* 4.3 21.2 - - + +
352A GLU 4.3 1.6 - - - +
353A ALA* 3.5 15.3 - - + -
354A THR* 3.1 43.9 + - + +
356A ASP* 1.4 74.6 - - + +
358A GLU* 1.3 61.7 + - - +
360A GLN* 3.3 6.0 + - - +
361A LEU* 3.1 25.5 + - - +
364A LYS* 5.3 11.6 + - - +
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A SER 4.4 10.2 - - - +
353A ALA* 3.8 21.8 - - + +
354A THR 3.0 18.7 + - - +
355A GLU* 3.5 14.2 - - - +
357A GLU* 1.3 77.1 - - - +
359A GLN* 1.4 60.1 + - - +
361A LEU* 4.0 4.3 + - - +
402A GLN* 3.3 12.8 - - - +
437A MET* 3.4 42.4 - - + +
438A CYS 4.3 3.3 - - - -
439A PRO* 3.6 38.9 - - - +
440A TYR* 4.4 2.3 + - - +
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Residues in contact with GLN 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLU 3.2 10.9 + - - +
356A ASP* 3.1 12.1 + - - +
358A GLU* 1.4 79.6 - - - +
360A GLN* 1.3 88.6 + - - +
362A LEU 4.5 0.3 + - - -
363A HIS* 3.4 15.0 + - - -
382A GLU* 2.7 35.7 + - - +
402A GLN* 2.7 31.0 + - - +
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Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASP* 3.0 19.2 + - + +
357A GLU* 3.3 6.4 + - - +
359A GLN* 1.3 102.1 + - - +
361A LEU* 1.3 63.9 + - - +
362A LEU 3.4 0.7 - - - -
363A HIS* 3.2 23.0 + - - +
364A LYS* 3.0 50.6 + - - +
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 3.9 24.9 - - + +
322A PHE* 3.7 28.5 - - + -
323A LEU* 3.9 24.9 - - + -
348A ILE* 3.6 32.1 - - + -
357A GLU 3.1 15.2 + - - +
358A GLU 4.3 7.6 - - - +
359A GLN 3.5 1.8 - - - -
360A GLN* 1.3 76.1 - - - +
362A LEU* 1.4 61.3 + - + +
364A LYS* 3.2 7.0 + - - +
365A VAL* 2.9 38.5 + - + +
437A MET* 3.7 13.7 - - - -
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ILE* 5.2 8.5 - - + -
359A GLN 4.5 1.8 + - - -
360A GLN 3.4 0.6 - - - -
361A LEU* 1.4 81.4 - - + +
363A HIS* 1.4 49.7 + - - +
365A VAL* 4.1 4.4 - - + +
366A THR* 2.7 41.6 + - - +
380A ILE* 4.4 10.5 - - + -
402A GLN* 3.8 36.5 + - + +
403A LYS* 3.9 35.0 - - - +
404A CYS* 4.0 11.7 - - + +
435A LEU* 3.8 38.1 - - + +
437A MET* 4.4 14.1 - - + +
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Residues in contact with HIS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLN* 3.4 35.2 + - - -
360A GLN* 3.2 23.0 + - - +
362A LEU* 1.4 74.5 - - - +
364A LYS* 1.4 58.7 + - + +
366A THR* 3.3 5.9 + - - -
367A ASP* 3.0 42.6 + - - +
380A ILE* 3.6 25.2 - - + +
382A GLU* 2.7 28.8 + - - -
402A GLN* 3.8 4.9 + - - -
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Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A PHE* 3.6 50.0 + - + +
357A GLU* 5.3 13.3 + - - +
360A GLN* 3.0 46.1 + - + +
361A LEU* 3.2 8.9 + - + +
363A HIS* 1.4 76.6 - - + +
365A VAL* 1.3 57.4 + - - +
367A ASP* 3.5 6.9 + - - +
368A PHE* 3.0 28.6 + - - +
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ALA* 3.8 31.6 - - + +
319A VAL* 3.9 18.6 - - + -
322A PHE* 3.8 12.3 - - + -
361A LEU* 2.9 25.3 + - + +
362A LEU* 4.1 6.5 - - + +
364A LYS* 1.3 76.8 - - - +
366A THR* 1.3 57.5 + - + +
368A PHE* 3.4 4.7 + - - +
369A TRP* 3.1 63.9 + - + -
435A LEU* 4.4 10.8 - - + -
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Residues in contact with THR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU 2.7 23.5 + - - +
363A HIS* 3.3 7.8 + - - -
365A VAL* 1.3 74.9 - - + +
367A ASP* 1.4 61.6 + - - +
369A TRP* 3.3 10.1 + - + +
370A LYS* 2.8 29.6 + - - +
375A LEU* 3.4 13.2 - - + +
378A CYS* 3.8 15.8 - - - -
380A ILE* 3.6 14.6 - - + +
404A CYS* 4.5 8.3 - - - -
406A LEU* 3.8 37.2 - - + -
435A LEU* 5.4 0.4 - - + -
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A HIS* 3.0 31.4 + - - +
364A LYS* 3.8 6.4 - - - +
366A THR* 1.4 76.5 + - - +
368A PHE* 1.3 57.2 + - - +
370A LYS* 3.2 20.3 + - - +
371A GLN* 2.9 43.3 + - + +
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Residues in contact with PHE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A GLU* 5.4 2.7 - - + -
318A ALA* 4.0 29.8 - - + -
321A THR* 5.2 13.2 - - + -
322A PHE* 3.9 19.3 - + + -
364A LYS 3.0 18.6 + - - +
365A VAL 3.4 3.8 - - - +
367A ASP* 1.3 74.8 - - - +
369A TRP* 1.4 76.2 + + - +
371A GLN* 3.4 18.1 + - - +
372A GLN* 3.0 61.0 + - + +
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Residues in contact with TRP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A LEU* 3.8 23.4 + - + +
315A VAL* 3.9 18.2 - - + -
318A ALA* 3.7 28.7 - - + +
365A VAL* 3.1 34.2 + - + -
366A THR* 3.3 12.3 + - + +
368A PHE* 1.4 87.6 - + - +
370A LYS* 1.3 59.9 + - - +
372A GLN* 3.1 4.8 + - + +
373A GLY 3.0 8.8 + - - -
374A LEU* 2.9 55.6 + - + +
375A LEU* 4.0 12.3 - - + +
406A LEU* 3.6 28.0 - - + -
408A LEU* 3.7 33.2 - - + -
435A LEU* 4.0 11.9 - - + -
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Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A THR 2.8 21.6 + - - +
367A ASP* 3.5 20.2 - - - +
369A TRP* 1.3 71.2 - - - +
371A GLN* 1.4 61.7 + - + +
373A GLY* 3.2 13.5 + - - -
375A LEU* 3.8 28.2 - - + +
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Residues in contact with GLN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A PHE* 6.3 0.2 - - - -
367A ASP* 2.9 37.7 + - + +
368A PHE* 3.5 17.4 - - + +
370A LYS* 1.4 75.2 - - + +
372A GLN* 1.3 66.5 + - - +
373A GLY 3.3 1.5 + - - -
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A PHE* 3.0 57.5 + - + +
369A TRP* 3.1 9.4 + - - +
371A GLN* 1.3 80.3 - - - +
373A GLY* 1.3 60.8 + - - +
374A LEU* 3.9 25.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il